From j.abbott at imperial.ac.uk Mon Mar 1 09:55:01 2004 From: j.abbott at imperial.ac.uk (James Abbott) Date: Mon Mar 7 02:29:51 2005 Subject: Problems with Pfam References: Message-ID: Guy Bottu wrote: > While trying to index under SRS the latest version (12.0) of the Pfam > databank I had a "malloc" error. It also occurs when I just do "icarus > pfam.is". Apparently some entries have become too big. The first > offending entry is GP120 (PF00516). Has anyoane of you met the same > problem ? Has anyone an idea about how to fix it ? Guy, This kind of error is normally the result of SRS trying too handle too much data at once, and can generally be solved by reducing the size of data by parallelising the build, or reducing the size of each part within an already parallelised library (see section 7.6.3 of the SRS Admin guide, page 119). Lion recently released an update pfam.i file which (available from http://downloads.lionbio.co.uk/parser/), which does just this for pfama. Try upgrading to the latest version of this file then try again. If you are still having problems, try reducing the partSizeKb parameter of the pfama $Library definition to further reduce the quantity of data being handled at once. Hope that helps, James -- Dr. James Abbott Bioinformatics Software Developer, Bioinformatics Support Service Imperial College, London From benedict.arnold at bbsrc.ac.uk Tue Mar 9 08:21:14 2004 From: benedict.arnold at bbsrc.ac.uk ("benedict arnold JIC) Date: Mon Mar 7 02:29:51 2005 Subject: Problems with Pfam Message-ID: Hi Guy, James has probably covered most of the things you can do vis-a-vis the Icarus side of things. Depending on what OS you are using you can also change the datasize limit on the machine, on OSF this is a common occurrence where the limits are set to ridiculously small values. We currently have the datasize hard limit set to 4Gb abd Pfam indexes no problems, usually upping the datasize parameter fixes most things. cheers Ben Arnold Computational Biology Support Specialist John Innes Centre Colney Lane Norwich NR4 7UH Dear colleagues, While trying to index under SRS the latest version (12.0) of the Pfam databank I had a "malloc" error. It also occurs when I just do "icarus pfam.is". Apparently some entries have become too big. The first offending entry is GP120 (PF00516). Has anyoane of you met the same problem ? Has anyone an idea about how to fix it ? Regards, Guy Bottu, Belgian EMBnet Node --- From suter at lionbioscience.com Thu Mar 11 01:06:33 2004 From: suter at lionbioscience.com (Dr. Clemens Suter-Crazzolara) Date: Mon Mar 7 02:29:51 2005 Subject: LION user group meeting Message-ID: <200403101019.i2AAJmu08341@admin05.lion-ag.de> The first annual LION User Group Meeting will be held at King's College in Cambridge, UK, May 10-12, 2004. This is a perfect networking opportunity to meet other LION software users, administrators and developers. Hear about new developments and case studies. To register or to receive more information about the user meeting, please go to: www.lionbioscience.com/ugm or contact ugm@lionbioscience.com. ---